py3dmol_example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "import py3Dmol\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.AddHs(Chem.MolFromSmiles('COC(C)C'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<rdkit.rdBase._vecti at 0x7fb6b55da4b0>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "AllChem.EmbedMultipleConfs(mol, 5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_16100989287101433\"  style=\"position: relative; width: 400px; height: 400px\">\n        <p id=\"3dmolwarning_16100989287101433\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n        </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_16100989287101433 = null;\nvar warn = document.getElementById(\"3dmolwarning_16100989287101433\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_16100989287101433 = $3Dmol.createViewer($(\"#3dmolviewer_16100989287101433\"),{backgroundColor:\"white\"});\n\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    1.7444    1.1038   -0.2485 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.6700    0.6905    0.4806 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1533   -0.2249   -0.0676 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.5175    0.4302   -0.2856 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.3737   -1.4860    0.6952 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    1.9145    0.8423   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.8050    0.3470    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1739   -0.1733   -0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.5752   -1.5802   -0.0880 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.4142    0.6923   -0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    2.0279   -0.2561   -0.1581 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.8692   -0.2103    0.6055 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2556    0.0894   -0.1169 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9409    1.3031    0.4735 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2159   -1.0729    0.0020 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n   -1.9896    0.2151    0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.7116    0.1986    0.7040 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2654   -0.0046   -0.2988 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.9201   -1.3388   -0.0245 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.2196    1.1316   -0.3730 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    2.0075   -0.4299   -0.4395 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.7464   -0.1625   -0.9424 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1946    0.0789    0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2693   -0.9844   -0.1204 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.8533    1.4308   -0.0963 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n\tviewer_16100989287101433.setStyle({\"stick\": {}});\nviewer_16100989287101433.render();\n});\n</script>",
      "text/html": [
       "<div id=\"3dmolviewer_16100989287101433\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "        <p id=\"3dmolwarning_16100989287101433\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
       "    tag.async = true;\n",
       "    tag.onload = () => {\n",
       "      resolve();\n",
       "    };\n",
       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
       "});\n",
       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_16100989287101433 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_16100989287101433\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_16100989287101433 = $3Dmol.createViewer($(\"#3dmolviewer_16100989287101433\"),{backgroundColor:\"white\"});\n",
       "\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    1.7444    1.1038   -0.2485 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.6700    0.6905    0.4806 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1533   -0.2249   -0.0676 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.5175    0.4302   -0.2856 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.3737   -1.4860    0.6952 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n",
       "\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    1.9145    0.8423   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.8050    0.3470    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1739   -0.1733   -0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.5752   -1.5802   -0.0880 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.4142    0.6923   -0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n",
       "\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    2.0279   -0.2561   -0.1581 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.8692   -0.2103    0.6055 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2556    0.0894   -0.1169 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9409    1.3031    0.4735 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2159   -1.0729    0.0020 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n",
       "\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n   -1.9896    0.2151    0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.7116    0.1986    0.7040 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2654   -0.0046   -0.2988 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.9201   -1.3388   -0.0245 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.2196    1.1316   -0.3730 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n",
       "\tviewer_16100989287101433.addModel(\"\\n     RDKit          3D\\n\\n  5  4  0  0  0  0  0  0  0  0999 V2000\\n    2.0075   -0.4299   -0.4395 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.7464   -0.1625   -0.9424 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1946    0.0789    0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2693   -0.9844   -0.1204 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.8533    1.4308   -0.0963 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  3  5  1  0\\nM  END\\n\",\"sdf\");\n",
       "\tviewer_16100989287101433.setStyle({\"stick\": {}});\n",
       "viewer_16100989287101433.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "p = py3Dmol.view(width=400,height=400)\n",
    "mol = Chem.RemoveHs(mol)\n",
    "for i in range(5):\n",
    "    \n",
    "    mb = Chem.MolToMolBlock(mol, confId=i)\n",
    "    p.addModel(mb, 'sdf')\n",
    "p.setStyle({'stick':{}})\n",
    "p.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.9"
  },
  "widgets": {
   "application/vnd.jupyter.widget-state+json": {
    "state": {},
    "version_major": 2,
    "version_minor": 0
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}

To run the code, please install rdkit and py3dmol.
$ conda install -c conda-forge rdkit
$ conda install -c conda-forge py3dmol

Works like a charm. Thanks!

Happy to hear that ;)